6GPG | pdb_00006gpg

Structure of the RIG-I Singleton-Merten syndrome variant C268F


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 
    0.260 (Depositor), 0.265 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6GPG

This is version 1.1 of the entry. See complete history

Literature

Unified mechanisms for self-RNA recognition by RIG-I Singleton-Merten syndrome variants.

Lassig, C.Lammens, K.Gorenflos Lopez, J.L.Michalski, S.Fettscher, O.Hopfner, K.P.

(2018) Elife 7

  • DOI: https://doi.org/10.7554/eLife.38958
  • Primary Citation Related Structures: 
    6GPG

  • PubMed Abstract: 

    The innate immune sensor retinoic acid-inducible gene I (RIG-I) detects cytosolic viral RNA and requires a conformational change caused by both ATP and RNA binding to induce an active signaling state and to trigger an immune response. Previously, we showed that ATP hydrolysis removes RIG-I from lower-affinity self-RNAs (Lässig et al., 2015), revealing how ATP turnover helps RIG-I distinguish viral from self-RNA and explaining why a mutation in a motif that slows down ATP hydrolysis causes the autoimmune disease Singleton-Merten syndrome (SMS). Here we show that a different, mechanistically unexplained SMS variant, C268F, which is localized in the ATP-binding P-loop, can signal independently of ATP but is still dependent on RNA. The structure of RIG-I C268F in complex with double-stranded RNA reveals that C268F helps induce a structural conformation in RIG-I that is similar to that induced by ATP. Our results uncover an unexpected mechanism to explain how a mutation in a P-loop ATPase can induce a gain-of-function ATP state in the absence of ATP.


  • Organizational Affiliation
    • Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.

Macromolecule Content 

  • Total Structure Weight: 90.94 kDa 
  • Atom Count: 5,812 
  • Modeled Residue Count: 677 
  • Deposited Residue Count: 742 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DDX58C [auth A]714Homo sapiensMutation(s): 1 
Gene Names: DDX58
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for O95786 (Homo sapiens)
Explore O95786 
Go to UniProtKB:  O95786
PHAROS:  O95786
GTEx:  ENSG00000107201 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95786
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*CP*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*CP*G)-3')A [auth B],
B [auth C]
14synthetic construct
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free:  0.260 (Depositor), 0.265 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.62α = 90
b = 175.62β = 90
c = 109.53γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyHO2489/8
German Research FoundationGermanyCRC1054 project B02

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Data collection, Database references, Structure summary